Mass Effect:the lost and forgotten
by Mr. Carnage
Summary: Recent events have taken their toll on commander Shepard's psyche, and now a new enemy may push him towards insanity. Can commander Shepard and his team defeat this long lost entity or will everything he knows and loves get swallowed around him and push him over the edge.
1. Chapter 1: Shepard's Mental Penance

**This is my first story so I would appreciate any feedback people could give me, Thank you ;)**

Chapter 1

He woke up with an ill feeling in the pit of his stomach, Shepard opened his eyes facing the roof of his luxury cabin quarters, he didn't want to think about it but the thought of what he did kept worming its way inside his brain.

"So many…" he thought, he started to move his right arm a little as he started getting lost in thought but panicked when it came into contact with a foreign fabric, than the one between his sheets.

He panic soon fleeted as his eyes laid upon her, he soon calmed down, Tali laid there fast asleep in full exosuit, Shepard knew he had to get used to the fact that unlike his other lovers from his not so clean past he would never wake up next to her without her clothes on out of risk of an allergic reaction, the two of them having sex was risky enough, "still she was always cute in her suit" he thought.

Happy thoughts were soon interrupted again as Ashley had found her way into his head also, "what the hell am I gonna do? "

After horizon he felt hurt, she had basically called him a betrayer, he wanted to kiss her instead he had basically received a slap in the face.

That in turn made him realize his feelings for Tali when she re-joined the crew, everything apart from the imminent reaper invasion and the collector problem was good again but after the so clled suicide mission from which they all survived he finally read that message from her "that damn message" he whispered to himself so Tali wouldn't wake.

_Subject: Hey there._

_Shepard-_

_I'm sorry for what I said back on Horizon. When I lost you two years ago, it tore me up. I prayed for you every day. I read a lot of Tennyson, thinking about you, just like I did when my dad passed. And then you came back, and it was like my prayers were answered. But I'm not who I was then, and neither are you._

_I don't know what's true anymore. Part of me can't believe it's really you. I keep going back to that night before Ilos, our night... I haven't let myself think about those memories in over a year._

_I wouldn't have expected you to work for Cerberus, but I know why they sent you to Horizon. I saw how many people were lost there, and if anyone can stop the Collectors, you can. I can't go where you're going, but I can wish you luck._

_Just stay alive out there... Skipper. I don't know what the future holds, but I can't lose you a second time._

_-Ash_

_Death closes all: but something ere the end_

_Some work of noble note, may yet be done,_

_Not unbecoming men that strove with Gods._

He remembered the feeling he had when he first read that message, guilt, an undeniable guilt that is still lingering within him, "ugh, I need a shower".

Shepard slowly got up and walked towards the shower hoping the water would be able to clear his head, but stopped when he realised that the noise would probably wake up Tali, so he put on some trousers sat down at his desk and decided to have a look through some data mission files, all the while thinking about what the impending future would soon have in store for him.

* * *

Legion began a new consensus:

Consensus: condition of Shepard, Commander

Legion took into account all the events that had recently transpired, destruction of collector base, disassociation with Cerberus, Batarian colony destruction incident also taking into account impending trial from earth and prominent reaper invasion.

As he started his consensus he became aware of another presence in the room, one that he could not see, his monitors detecting very light breathing and a faint heartbeat, immediately he came to a consensus to who the other being in the room was.

"Kasumi Goto do you require to speak to us?"

Kasumi let out an annoyed grunt "Damn you always know I'm there" she said with a small natural smile on her face.

Legion fully turned towards her now "of course we wer…"

"I know I know you can detect my heartbeat blah blah blah" she said playfully.

"Yes I did want to talk to you actually, what do you plan on doing when Shep gets called down for the trial on earth".

"Clarify" if the geth could give a confused look he would indeed be giving one right now.

"Well you see no one out the main fighting group is really sticking around to be with Shepard when he has to go down there for the trial, sounds harsh but everyone has their reasons".

"Clarify" the geth repeated, Kasumi thought for a moment and then realised what to say.

"oh you mean what is everyone doing?" she lightly slapped her forehead thinking how obvious it was and how obvious it was to be a little curious.

"well I have my eyes on a new prize, can't go into details I'm afraid" Legion knew about Kasumi's colourful past but the geth could not make a consensus on if this made her a threat, he recognised that as she was part of the crew this indeed made her an ally, Kasumi continued..

"Jacob and Miranda can't go back to Cerberus after basically defecting from Cerberus and they can't go to earth because they'll be arrested for being Cerberus employees all they can do is wander at this time" Legion understood, it made logical sense that both parties would not welcome them.

"Jack is going to do whatever Jack does, Thane is going to go to the citadel to pick up his son so they can go to a desert together" Jack was a similar situation as Kasumi to Legion, he could not tell if she was a threat but reached the consensus of Ally, he knew Thane wanted to go to the desert for medical reasons.

"Zaeed has a new mercenary job offer, Samara has already returned to Asari space because of her justicar code, Mordin actually might be returning to STG even after the Genophage thing and Grunt has gone back to Tuchanka to become a solider for urdnot Wrex" while Kasumi was explaining, Legion was processing the data Kasumi was giving him deciding on what he should do also.

"Hell even Garrus and Tali aren't sticking around, Garrus is going to try and convince the Turian Primarch that the reapers are real and a serious threat and Tali has her duties to the Quarian fleet, she's also got to rebuild her reputation after being accused of being a traitor" Legion was surprised (if a geth can be surprised) that creator Tali Zorah was not staying with Shepard commander especially after their recent acknowledgment of their feelings but again it made logical sense to return to the fleet as she could be considered no longer part of the fleet if she is gone too long.

"So back to the original question, what are you doing when this is all over, I mean I doubt they would be happy letting a geth come onto earth" Legion knew this to be true, relations between geth's and organics were not good especially between them and the creators suddenly he reached a consensus.

"we will return to the geth and give our findings, we will most likely prepare for war" Kasumi nodded her head "no rest for the wicked huh?" legion quickly looked up the term.

"Human phrase derives from…" Kasumi putout her hand.

"please don't explain it I know exactly what it means".

"acknowledged" Legoin then turned away from Kasumi and started to continue on with his original presuming the conversation was finished.

"well I'll see you later Legion I suppose, hmmm maybe I should try and steal Garrus's calibration code before I leave, could be worth something" and just like that, the Japanese thief vanished from sight.

* * *

The atmosphere down in the lower engineering room was a more positive one; Joker, Garrus, Zaeed, Jack and Thane were all playing the earth game poker.

A tradition that had been started by gabby, Ken, Shepard and Tali was now being continued by Joker ever since he heard them play over the intercom, every so often Joker would ask the rest of the crew if anyone was interested, and today was another one of these sessions.

The regulars were the original group, Jack, Zaeed and Garrus however gabby and ken were busy with their duties and Shepard and Tali were sleeping, the group were surprised to be joined by Thane this time round but none said anything about it.

As the game progressed all were lost focused on winning with their respective hands, with Joker constantly giving away if he had a good hand or not by smiling, but Garrus was distracted from the game, he was worried about Shepard's mental condition after the recent events.

"I wonder if he's okay" he said aloud.

"If who's okay?" asked Thane.

"You know, Shepard after the Batarian thing".

"Ah I see, yes I must imagine it is quite stressful on his mind" Zaeed decided to interject.

"yeah messy business, in my rookie days I was part of a team to take out a whole Asari colony on an uncharted world who were illegally taking minerals, children and all, it was damn awful but in all my years I never did anything near the level of what Shepard did" Joker felt the sudden need to stick for his long time commander.

"yeah but what choice did he have, either that or get the reaper invasion when no one's even ready"

Jack had become annoyed with the conversation fast.

"Fuck, let's not turn this into the Shepard pity party alright, c'mon were still playing a game you know".

Everyone returned their eyes to the game but Garrus hadn't been reassured on his commanders well-being he was now even more worried than he had been initially had been "you know what you guys keep playing I'm out" Garrus got up and turned to leave, Joker decided to be a bit opportunistic.

"Well no point leaving his chips to waste" as joker reached out for Garrus's chips Jack suddenly slammed her biotic fist down.

"Touch them and I'll smear your blood against the wall, and I don't need to put in much power, cause your easy to break" as the argument began thane watched Garrus walk towards the elevator, he wasn't good at counselling people but this time he felt the need to act.

"Jack you may have my chips, thank you everyone for the game" Thane quickly headed after Garrus, Zaeed suddenly realised something.

"Right, who the bloody hell is going to give me their chips" the argument continued.

* * *

Meanwhile…

He knew he was the last one left, he didn't know how he could be seeing this, the same act carried out over and over again but in various gruesome ways.

He couldn't bear to watch it any longer, he finished his recording hoping the next group to come would find and get out as soon as they could, he picked up his gun, put it against his head and fired it…

The last sound that could be heard was a slither…

**Again please say what you liked and what you didn't like thank you, constructive critism welcome; again this is only the first chapter!**


	2. Chapter 2: A Turian, A Geth and a Drell

**I made some changes in the first chapter, namely dialogue spaced out and fixed the writing, now it says that both Grunt and Samara have already left.**

**This Story has ironically become a side project, this was originally my main project however what was originally my side project My Little Pony: friendship is murder now has my main focus, so this story we be updated less regularly however reviews will convince me too update more often whether they be positive or not.**

Chapter 2: A Turian, a Geth and a Drell

Garrus needed to talk to Shepard now, he had known this man for a long time and had become one of his most trusted friends but there was something truly wrong with him.

Shepard had a tendency to visit all of his crew on a regular basis, out of all the other commanders he had ever known, none would have taken the time out of their busy schedule to do the same as he does but now no one ever saw him unless he called everyone to a meeting _"and maybe Tali…"_ he thought.

As he was about to enter through the elevator door he was surprised by a voice from behind him calling his name, "Garrus!"

As he turned around he found that Thane was walking up to him with a steady pace and his hands placed behind his back, this kind of behaviour always tended to make Garrus nervous, like someone was about to stab him in the back, he always liked to see the persons hands where he could see them, maybe this habit was from his c-sec days or maybe this was from the betrayal on Omega, either way he couldn't complain as Thane could be seen like this often when walking.

"Can I help you with something Thane?"

"Yes, you seem…troubled and I feel that we should talk"

He had never known Thane to be someone to confide in, Shepard was the one to convince him to talk to the other members of the crew in the first place however he decided to humour him this time round.

"Alright then…let's walk and talk"

The two men started to enter the elevator when Thane stated "you're worried about Shepard, am I correct in saying"

Before Garrus could press the elevator to go up he paused on hearing Thane's sentence, he closed his eyes and breathed a heavy sigh "Yeah I am I think you've also seen that there's something clearly wrong with him and we both know what it is"

"Yes the Batarian incident"

"Not only that, he is now going to be tried by his own people, who knows what is going to happen with that"

Thane decided to risk upsetting Garrus on a point that had made him curious, "then if you indeed do not mind me saying, why are you leaving to have Shepard face it alone?"

As Garrus was finally about to press the button to Shepard's quarters, the question surprised him and he accidently pressed the button to go the 2nd deck without realising "what do you mean?"

"No one is staying for one reason or another but you of all people I would have thought would have stayed and supported him"

As the elevator doors closed and they began to move Garrus had been offended by the comment that Thane had just made, he became somewhat defensive "funny that coming from you, you know because you'd probably jump off a malfunctioning ship before even the woman and children leave, what's the human expression, the pot calling the kettle black".

Garrus knew that kind of behaviour was nothing like Thane but he was merely trying to get a rise out of him and move the conversation away from why he's leaving, Thane remained completely composed as ever so it appeared that it hadn't work.

Thane wasn't sure what the expression meant (and neither did Garrus entirely) but he mostly understood the meaning behind it "I might have actually stayed but Shepard was extremely persistent that I spend time with my son before the reapers arrive, but you are avoiding the question at hand why are you not staying by his side?"

"You know this conversation more applies to Tali surely, so maybe you shou…"

"Garrus!"

Garrus was taken aback by the sudden aggresive rise in tone in Thane's voice, he (and he didn't think anyone else) had ever heard him like that before, he knew he was indeed avoiding the question, he wasn't even sure really why but maybe he felt somewhat guilty "I'm going to the Turian Primarch back on Palavin to try and convince him the danger of the reaper threat and make him take some form of precaution"

Thane gave Garrus a suspicious look "that may be so but that is not the only reason is it?"

Garrus looked down on the floor "No your right"

He then looked up to the ceiling almost reminiscing "when I first left with Shepard I didn't leave on great terms with my father, I want to see my family again my dad and sister, hell my dad could help me get to the Primarch but I just want to see them again before, well you know".

Thane paused for a moment and then he spoke "I apologise, I can indeed sympathise with wanting to reconnect with family".

As the two men stopped talking they realised they were not at Shepard's quarters but they were on the second deck, not only that but the elevator door was open and there stood Legion who they both presumed was there the entire time, an awkward silence followed…

Tali woke in a daze, she wasn't sure where she was, all she knew was that her face was planted against the side of her mask and it felt really uncomfortable.

She dared to lift her head in order to view her surroundings and get an idea exactly where she was and as soon as she did she knew that she was in Shepard's room and with that all the memories from the night before flooded back into her mind, but she realised that one piece of the puzzle was missing, "Shepard, where are you?"

She received no answer, Tali knew he had to be on the ship somewhere, but she could not help but worry, it wasn't lost on Tali either that there was something seriously wrong with Shepard as of late she knew he must also must be feeling very lonely right now having only Joker at his side when he returns to earth to face the trial.

She so desperately wanted to be with him when he got there but now her people needed her more than ever, they were potentially on the verge of a war with the Geth, a war she knew that they could not win, they called her back for one reason or another and Aunty Raan seemed especially desperate for her to return.

She looked around the room but this time she was able to hear the faint sound of water running in the shower "ah, so that's where you are".

She said it in a seductively tone with a mischievous grin on her face (one she knew no one could see) she thought about the possibility of jumping in there with him, however she wasn't sure what mood he was in today as they had been on and off constantly as of late and it wasn't safe for her to be out of her suit so soon and without precautions, in the end she sided against it and then decided to at least get out of bed.

She walked over to the desk to see quite a number of data pads scattered all over the desk, as she peered across they were all battle strategies and whatever Reaper statistics that were available (which were not a lot) she sighed as she picked up one to peer over it, "oh keelah Shepard, you're going worry yourself to death over this aren't you".

She flicked through it a little till her attention was drawn to a door opening close and Shepard walking out with only a towel around his waist, "Hey Shepard, good morning".

Shepard looked at what Tali was holding and he displayed a cross look "Tali what are you doing?"

"Oh I was just looking, your desk was a real mess and I was curi…"

"That isn't something for you to mess around with ok, put it back".

"Hey I wasn't messing around with anything I was just looki…"

"TALI, PUT IT BACK!"

Tali immediately dropped the data pad on the desk and stepped a few spaces away from Shepard, she was shocked, Shepard had never shouted at her before and she didn't really know how to react.

Shepard just put his head in his hands, and let out a long sigh "I'm sorry, I didn't mean to shout".

Tali was still cautious but decided to respond "no, that was my fault I should have just left it alone, I didn't know it would upset you that much".

Shepard reached out to Tali and brought her into a hug "I'm sorry I shouldn't have shouted like that, I don't know what's wrong with me lately but I promise you that I'm going to figure it all out and then I'll be back to normal, kay?"

"Kay"

The two stayed there for a while, holding each other in embrace, quietly musing too themselves what exactly did the future have in store for them.

The three of them had been standing there facing each other for about a minute at this point in utter silence, Garrus had decided to break this awkward tension between the three of them "Legion…can I help you with something?"

Legion looked directly at Garrus and simply replied "No".

The awkward silence immediately returned for ten more seconds, Thane was in no way phased by this as he was use to the quiet but Garrus could not take it "So what are you doing right now".

"We currently need data in order to finish a consensus, the only one who possess the necessary information is Shepard Commander".

Garrus took in the fact that the Geth wanted to see Shepard but knew he was going to have to burst the Geth's bubble as he had to see him first "well you'll have to get in line, I need to talk to Shepard right now about something important".

The Geth boldly walked in and pressed the button to Shepard's quarters and the elevator doors closed in front of them "we regret to inform you that we must take priority with Shepard Commander, it is crucial to his wellbeing".

Garrus turned to the Geth "you don't regret it, you don't feel anything, I think Shepard is a little busy, so I doubt he'd have time to help you with another one of your consensus".

The Geth was unfazed by this and simply remained silent, Thane attempted to defuse the situation before it became violent "why don't we all calmly go to Shepard and talk to him together".

Garrus turned to him "I've known Shepard for two years now, this Geth hasn't been here nearly long enough to decide who needs to talk to Shepard more".

This caught Legion's attention "you do not acquire hardware which allows you to examine Organics becoming troubled, we do, logically we should be the one to talk to Shepard Commander about his potentially troubled mental state".

Garrus was slightly calmer now, "Legion I really don't think he needs advice from a being that doesn't even feel emotion".

The argument continued as the elevator headed towards Shepard's quarters.

The silence in Shepard's room was hard to stand for Tali, they had broken their embrace a minute after it started and she was just sitting at the foot of his bed while he had gotten changed in his uniform and was looking through his files again, she needed to say something but the only thing she could think of might send Shepard off again, however she knew that she had no choice in the matter "so what is in the files?"

She already knew what was in them when she took a peak but again she had to say something, Shepard slowly turned to face her, he showed no expression on his face, "some contain all the information that we know about the reapers and some are battle strategies I have drawn up to face them".

She asked something out of curiosity "anything in there that you think would be effective".

Shepard simply buried his head in his hands and said "nothing that I'm sure on".

The silence was about to creep in on the two of them again but Shepard was the one to try and stop it this time "Tali, look I'm…"

Shepard had been interrupted by the sound of his door opening, the two saw Garrus, thane and Legion stride into their room, legion was the first one to speak "Shepard Commander, we must speak to you about…"

Garrus immediately cut the Geth off "no I need to talk to him, you can wait your turn and…"

"We have already stated the reasons we should talk first, why would you persist on…"

"Because your reasons are crap Legion, I understand him more and…"

"ALL OF YOU SHUT UP!"

Everyone froze on Shepard's outburst, it was quiet enough to hear a pin drop, Shepard did the best he could to compose himself "okay, what do you want Garrus?"

"Uh…I wanted to talk to you because…I was worried about you"

Garrus appeared to be somewhat embarrassed now, he thought about it and realised the whole argument with legion was nothing but silly, "Thane why are you here?"

Thane thought about it for a second, "Actually, I do not know".

Thane proceeded to walk out the door of the room, Shepard was understandably confused "okay then…legion what do you need to talk to me about?"

"Shepard Commander we must…"

Legion was cut off by EDI's voice over the intercom "Shepard, Admiral Hackett is requesting to speak with you, shall I set up communications in the debriefing room?"

"_Hackett why is he calling?"_he thought to himself, "I'm sorry everyone I have to go, and Garrus I'm fine, don't worry okay".

Garrus simply saluted and Shepard made his way to the debriefing room to see what Admiral Hackett needed from the commander.

**Again please say what you liked and what you didn't like thank you, Praise + constructive critism welcome! It will only make me better, again this will updated eventually, however it may be a little bit till then depending on the reviews and how far I get in my other story which I recommend anyone who likes the show to read and review also, I have gotten very positive feedback so far ;)**


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